Nematodes (derived from the Greek word for thread) are active, flexible, elongate, organisms that live on moist surfaces or in liquid environments, including films of water within soil and moist tissues within other organisms. While only 20,000 species of nematode have been identified, it is estimated that 40,000 to 10 million actually exist. Some species of nematodes have evolved as very successful parasites of both plants and animals and are responsible for significant economic losses in agriculture and livestock and for morbidity and mortality in humans (Whitehead (1998) Plant Nematode Control. CAB International, New York).
Nematode parasites of plants can inhabit all parts of plants, including roots, developing flower buds, leaves, and stems. Plant parasites are classified on the basis of their feeding habits into the broad categories: migratory ectoparasites, migratory endoparasites, and sedentary endoparasites. Sedentary endoparasites, which include the root knot nematodes (Meloidogyne) and cyst nematodes (Globodera and Heterodera) induce feeding sites and establish long-term infections within roots that are often very damaging to crops (Whitehead, supra). It is estimated that parasitic nematodes cost the horticulture and agriculture industries in excess of $78 billion worldwide a year, based on an estimated average 12% annual loss spread across all major crops. For example, it is estimated that nematodes cause soybean losses of approximately $3.2 billion annually worldwide (Barker et al. (1994) Plant and Soil Nematodes: Societal Impact and Focus for the Future. The Committee on National Needs and Priorities in Nematology. Cooperative State Research Service, US Department of Agriculture and Society of Nematologists). Several factors make the need for safe and effective nematode controls urgent. Continuing population growth, famines, and environmental degradation have heightened concern for the sustainability of agriculture, and new government regulations may prevent or severely restrict the use of many available agricultural anthelmintic agents.
The situation is particularly dire for high value crops such as strawberries and tomatoes where chemicals have been used extensively to control soil pests. The soil fumigant methyl bromide has been used effectively to reduce nematode infestations in a variety of these specialty crops. It is however regulated under the U.N. Montreal Protocol as an ozone-depleting substance and is scheduled for elimination in 2005 in the US (Carter (2001) California Agriculture, 55(3):2). It is expected that strawberry and other commodity crop industries will be significantly impacted if a suitable replacement for methyl bromide is not found. Presently there are a very small array of chemicals available to control nematodes and they are frequently inadequate, unsuitable, or too costly for some crops or soils (Becker (1999) Agricultural Research Magazine 47(3):22-24; U.S. Pat. Nos. 6,048,714). The few available broad-spectrum nematicides such as Telone (a mixture of 1,3-dichloropropene and chloropicrin) have significant restrictions on their use because of toxicological concerns (Carter (2001) California Agriculture, Vol. 55(3):12-18).
Fatty acids are a class of natural compounds that have been investigated as alternatives to the toxic, non-specific organophosphate, carbamate and fumigant pesticides (Stadler et al. (1994) Planta Medica 60(2):128-132; U.S. Pat. Nos. 5,192,546; 5,346,698; 5,674,897; 5,698,592; 6,124,359). It has been suggested that fatty acids derive their pesticidal effects by adversely interfering with the nematode cuticle or hypodermis via a detergent (solubilization) effect, or through direct interaction of the fatty acids and the lipophilic regions of target plasma membranes (Davis et al. (1997) Journal of Nematology 29(4S):677-684). In view of this general mode of action it is not surprising that fatty acids are used in a variety of pesticidal applications including as herbicides (e.g., SCYTHE by Dow Agrosciences is the C9 saturated fatty acid pelargonic acid), as bactericides and fungicides (U.S. Pat. Nos. 4,771,571; 5,246,716) and as insecticides (e.g., SAFER INSECTICIDAL SOAP by Safer, Inc.).
The phytotoxicity of fatty acids has been a major constraint on their general use in agricultural applications (U.S. Pat. No. 5,093,124) and the mitigation of these undesirable effects while preserving pesticidal activity is a major area of research. The esterification of fatty acids can significantly decrease their phytotoxicity (U.S. Pat. Nos. 5,674,897; 5,698,592; 6,124,359). Such modifications can however lead to dramatic loss of nematicidal activity as is seen for linoleic, linolenic and oleic acid (Stadler et al. (1994) Planta Medica 60(2):128-132) and it may be impossible to completely decouple the phytotoxicity and nematicidal activity of pesticidal fatty acids because of their non-specific mode of action. Perhaps not surprisingly, the nematicidal fatty acid pelargonic acid methyl ester (U.S. Pat. Nos. 5,674,897; 5,698,592; 6,124,359) shows a relatively small xe2x80x9ctherapeutic windowxe2x80x9d between the onset of pesticidal activity and the observation of significant phytotoxicity (Davis et al. (1997) J Nematol 29(4S):677-684). This is the expected result if both the phytotoxicity and the nematicidial activity derive from the non-specific disruption of plasma membrane integrity. Similarly the rapid onset of pesticidal activity seen with many nematicidal fatty acids at therapeutic concentrations (U.S. Pat. Nos. 5,674,897; 5,698,592; 6,124,359) suggests a non-specific mechanism of action, possibly related to the disruption of membranes, action potentials and neuronal activity.
Ricinoleic acid, the major component of castor oil, provides another example of the unexpected effects esterification can have on fatty acid activity. Ricinoleic acid has been shown to have an inhibitory effect on water and electrolyte absorption using everted hamster jejunal and ileal segments (Gaginella et al. (1975) J Pharmacol Exp Ther 195(2):355-61) and to be cytotoxic to isolated intestinal epithelial cells (Gaginella et al. (1977) J Pharmacol Exp Ther 201(1):259-66). These features are likely the source of the laxative properties of castor oil which is given as a purgative in humans and livestock. In contrast, the methyl ester of ricinoleic acid is ineffective at suppressing water absorption in the hamster model (Gaginella et al. (1975) J Pharmacol Exp Ther 195(2):355-61). (N.B. Castor oil is a component of some de-worming protocols because of its laxative properties.)
The macrocyclic lactones (e.g., avermectins and milbemycins) and delta-toxins from Bacillus thuringiensis (Bt) are chemicals that in principle provide excellent specificity and efficacy and should allow environmentally safe control of plant parasitic nematodes. Unfortunately, in practice, these two approaches have proven less effective for agricultural applications against root pathogens. Although certain avermectins show exquisite activity against plant parasitic nematodes these chemicals are hampered by poor bioavailability due to their light sensitivity, degradation by soil microorganisms and tight binding to soil particles (Lasota and Dybas (1990) Acta Leiden 59(1-2):217-225; Wright and Perry (1998) Musculature and Neurobiology. In: The Physiology and Biochemistry of Free-Living and Plant-parasitic Nematodes (eds R. N. Perry and D. J. Wright), CAB International 1998). Consequently despite years of research and extensive use against animal parasitic nematodes, mites and insects (plant and animal applications), macrocyclic lactones (e.g., avernectins and milbemycins) have never been commercially developed to control plant parasitic nematodes in the soil.
Bt delta toxins must be ingested to affect their target organ the brush border of midgut epithelial cells (Marroquin et al. (2000) Genetics. 155(4):1693-1699). Consequently they are not anticipated to be effective against the dispersal, non-feeding, juvenile stages of plant parasitic nematodes in the field. These juvenile stages only commence feeding when a susceptible host has been infected, thus to be effective nematicides may need to penetrate the cuticle. In addition, soil mobility of a relatively large 65-130 kDa proteinxe2x80x94the size of typical Bt delta toxinsxe2x80x94is expected to be poor and delivery in planta is likely to be constrained by the exclusion of large particles by the feeding tube of certain plant parasitic nematodes such as Heterodera (Atkinson et al. (1998) Engineering resistance to plant-parasitic nematodes. In: The Physiology and Biochemistry of Free-Living and Plant-parasitic Nematodes (eds R. N. Perry and D. J. Wright), CAB International 1998).
Many plant species are known to be highly resistant to nematodes. The most well documented of these include marigolds (Tagetes spp.), rattlebox (Crotalaria spectabilis), chrysanthemums (Chrysanthemum spp.), castor bean (Ricinus communis), margosa (Azardiracta indica), and many members of the family Asteraceae (family Compositae) (Hackney and Dickerson. (1975) J Nematol 7(1):84-90). The active principle(s) for this nematicidal activity has not been discovered in all of these examples and no plant-derived products are sold commercially for control of nematodes. In the case of the Asteraceae, the photodynamic compound alpha-terthienyl has been shown to account for the strong nematicidal activity of the roots. Castor beans are plowed under as a green manure before a seed crop is set. However, a significant drawback of the castor plant is that the seed contains toxic compounds (such as ricin) that can kill humans, pets, and livestock and is also highly allergenic.
There remains an urgent need to develop environmentally safe, target-specific ways of controlling plant parasitic nematodes. In the specialty crop markets, economic hardship resulting from nematode infestation is highest in strawberries, bananas, and other high value vegetables and fruits. In the high-acreage crop markets, nematode damage is greatest in soybeans and cotton. There are however, dozens of additional crops that suffer from nematode infestation including potato, pepper, onion, citrus, coffee, sugarcane, greenhouse ornamentals and golf course turf grasses.
Nematode parasites of vertebrates (e.g., humans, livestock and companion animals) include gut roundworms, hookworns, pinworms, whipworms, and filarial worms. They can be transmitted in a variety of ways, including by water contamination, skin penetration, biting insects, or by ingestion of contaminated food.
In domesticated animals, nematode control or xe2x80x9cde-wormingxe2x80x9d is essential to the economic viability of livestock producers and is a necessary part of veterinary care of companion animals. Parasitic nematodes cause mortality in animals (e.g., heartworm in dogs and cats) and morbidity as a result of the parasites"" inhibiting the ability of the infected animal to absorb nutrients. The parasite-induced nutrient deficiency results in diseased livestock and companion animals (i.e., pets), as well as in stunted growth. For instance, in cattle and dairy herds, a single untreated infection with the brown stomach worm can permanently stunt an animal""s ability to effectively convert feed into muscle mass or milk.
Two factors contribute to the need for novel anthelmintics and vaccines for control of parasitic nematodes of animals. First, some of the more prevalent species of parasitic nematodes of livestock are building resistance to the anthelmintic drugs available currently, meaning that these products will eventually lose their efficacy. These developments are not surprising because few effective anthelmintic drugs are available and most have been used continuously. Presently a number of parasitic species has developed resistance to most of the anthelmintics (Geents et al. (1997) Parasitology Today 13:149-151; Prichard (1994) Veterinary Parasitology 54:259-268). The fact that many of the anthelmintic drugs have similar modes of action complicates matters, as the loss of sensitivity of the parasite to one drug is often accompanied by side resistancexe2x80x94that is, resistance to other drugs in the same class (Sangster and Gill (1999) Parasitology Today Vol. 15(4):141-146). Secondly, there are some issues with toxicity for the major compounds currently available.
Human infections by nematodes result in significant mortality and morbidity, especially in tropical regions of Africa, Asia, and the Americas. The World Health Organization estimates 2.9 billion people are infected with parasitic nematodes. While mortality is rare in proportion to total infections (180,000 deaths annually), morbidity is tremendous and rivals tuberculosis and malaria in disability adjusted life year measurements. Examples of human parasitic nematodes include hookworm, filarial worms, and pinworms. Hookworm is the major cause of anemia in millions of children, resulting in growth retardation and impaired cognitive development. Filarial worm species invade the lymphatics, resulting in permanently swollen and deformed limbs (elephantiasis) and invade the eyes causing Aftican Riverblindness. Ascaris lumbricoides, the large gut roundworm infects more than one billion people worldwide and causes malnutrition and obstructive bowl disease. In developed countries, pinworms are common and often transmitted through children in daycare.
Even in asymptomatic parasitic infections, nematodes can still deprive the host of valuable nutrients and increase the ability of other organisms to establish secondary infections. In some cases, infections can cause debilitating illnesses and can result in anemia, diarrhea, dehydration, loss of appetite, or death.
While public health measures have nearly eliminated one tropical nematode (the water-borne Guinea worm), cases of other worm infections have actually increased in recent decades. In these cases, drug intervention provided through foreign donations or purchased by those who can afford it remains the major means of control. Because of the high rates of reinfection after drug therapy, vaccines remain the best hope for worm control in humans. There are currently no vaccines available.
Until safe and effective vaccines are discovered to prevent parasitic nematode infections, anthelmintic drugs will continue to be used to control and treat nematode parasitic infections in both humans and domestic animals. Finding effective compounds against parasitic nematodes has been complicated by the fact that the parasites have not been amenable to culturing in the laboratory. Parasitic nematodes are often obligate parasites (i.e., they can only survive in their respective hosts, such as in plants, animals, and/or humans) with slow generation times. Thus, they are difficult to grow under artificial conditions, making genetic and molecular experimentation difficult or impossible. To circumvent these limitations, scientists have used Caenorhabidits elegans as a model system for parasitic nematode discovery efforts.
C. elegans is a small free-living bacteriovorous nematode that for many years has served as an important model system for multicellular animals (Burglin (1998) Int. J. Parasitol., 28(3): 395-411). The genome of C. elegans has been completely sequenced and the nematode shares many general developmental and basic cellular processes with vertebrates (Ruvkin et al. (1998) Science 282: 2033-41). This, together with its short generation time and ease of culturing, has made it a model system of choice for higher eukaryotes (Aboobaker et al. (2000) Ann. Med. 32: 23-30).
Although C. elegans serves as a good model system for vertebrates, it is an even better model for study of parasitic nematodes, as C. elegans and other nematodes share unique biological processes not found in vertebrates. For example, unlike vertebrates, nematodes produce and use chitin, have gap junctions comprised of innexin rather than connexin and contain glutamate-gated chloride channels rather than glycine-gated chloride channels (Bargmann (1998) Science 282: 2028-33). The latter property is of particular relevance given that the avermectin class of drugs is thought to act at glutamate-gated chloride receptors and is highly selective for invertebrates (Martin (1997) Vet. J. 154:11-34).
A subset of the genes involved in nematode specific processes will be conserved in nematodes and absent or significantly diverged from homologues in other phyla. In other words, it is expected that at least some of the genes associated with functions unique to nematodes will have restricted phylogenetic distributions. The completion of the C. elegans genome project and the growing database of expressed sequence tags (ESTs) from numerous nematodes facilitate identification of these xe2x80x9cnematode specificxe2x80x9d genes. In addition, conserved genes involved in nematode-specific processes are expected to retain the same or very similar functions in different nematodes. This functional equivalence has been demonstrated in some cases by transforming C. elegans with homologous genes from other nematodes (Kwa et al. (1995) J. Mol. Biol. 246:500-10; Redmond et al. (2001) Mol. Biochem. Parasitol. 112:125-131). This sort of data transfer has been shown in cross phyla comparisons for conserved genes and is expected to be more robust among species within a phylum. Consequently, C. elegans and other free-living nematode species are likely excellent surrogates for parasitic nematodes with respect to conserved nematode processes.
Many expressed genes in C. elegans and certain genes in other free-living nematodes can be xe2x80x9cknocked outxe2x80x9d genetically by a process referred to as RNA interference (RNAi), a technique that provides a powerful experimental tool for the study of gene function in nematodes (Fire et al. (1998) Nature 391(6669):806-811; Montgomery et al. (1998) Proc. Natl. Acad. Sci. USA 95(26):15502-15507). Treatment of a nematode with double-stranded RNA of a selected gene can destroy expressed sequences corresponding to the selected gene thus reducing expression of the corresponding protein. By preventing the translation of specific proteins, their functional significance and essentiality to the nematode can be assessed. Determination of essential genes and their corresponding proteins using C. elegans as a model system will assist in the rational design of anti-parasitic nematode control products.
The invention features nucleic acid molecules encoding M. incognita malate dehydrogenase (MDH) and other nematode MDH-like polypeptides. M. incognita is a root knot nematode that causes substantial damage to crops, particularly to cotton, tobacco, pepper, and tomato. In part, the MDH-like nucleic acids and polypeptides of the invention allow for the identification of a nematode species, and for the identification of compounds that bind or alter the activity of MDH-like polypeptides. Such compounds may provide a means of combating diseases and infestations caused by nematodes, particularly by M. incognita, e.g., in tobacco, cotton, pepper or tomato plants.
The invention is based, in part, on the identification of a cDNA (complimentary DNA) encoding M. incognita MDH1 (SEQ ID NO:1). This 1327 nucleotide cDNA has a 1098 nucleotide open reading frame (SEQ ID NO:5) encoding a 366 amino acid polypeptide (SEQ ID NO:3). The invention is also based, in part, on the identification of a cDNA encoding M. incognita MDH2 (SEQ ID NO:2). This 2068 nucleotide cDNA has a 1098 nucleotide open reading frame (SEQ ID NO:6) encoding a 366 amino acid polypeptide (SEQ ID NO:4).
In one aspect, the invention features novel nematode malate dehydrogenase (MDH)-like polypeptides. Such polypeptides include purified polypeptides having the amino acid sequences set forth in SEQ ID NO:3 and SEQ ID NO:4. Also included are polypeptides having an amino acid sequence that is at least about 60%, 70%, 75%, 80%, 85%, 90%, 95%, or 98% identical to SEQ ID NO:3 and/or 4. The purified polypeptides can be encoded by a nematode gene, e.g., a nematode other than C. elegans. For example, the purified polypeptide have a sequence other than SEQ ID NO:7 or 8 (C. elegans MDH1 and MDH2 respectively). The purified polypeptides can further include a heterologous amino acid sequence, e.g., an amino-terminal or carboxy-terminal sequence derived from a different polypeptide. Also featured are purified polypeptide fragments of the aforementioned MDH-like polypeptides, e.g., a fragment comprising at least about 40, 50, 75, 100, 150, 189, 191, 200, 250, 300, or 355 amino acids of SEQ ID NO:3; SEQ ID NO:4, or the amino acid sequence of some other MDH-like polypeptide other than C. elegans MDH1 or MDH2. Non-limiting examples of such fragments include: fragments comprising about amino acid 1 to 149, 1 to 200, 1 to 223, 100 to 223, 149 to 223, 149 to 336, 200 to 366, and 223 to 366 of SEQ ID NO:3 and 4. The polypeptide or fragment thereof can be modified, e.g., processed, truncated, modified (e.g. by glycosylation, phosphorylation, acetylation, myristylation, prenylation, palmitoylation, amidation, addition of glycerophosphatidyl inositol), or any combination of the above. Also within the invention are polypeptides consisting of or consisting essentially of such fragments.
Certain MDH-like polypeptides comprise a sequence of 371 amino acids or fewer.
In another aspect, the invention features novel isolated nucleic acid molecules encoding a nematode MDH-like polypeptide. Such isolated nucleic acid molecules include nucleic acids having the nucleotide sequence set forth in SEQ ID NO:1, SEQ ID NO:2, SEQ ID NO:5, or SEQ ID NO:6. Also included are isolated nucleic acid molecules having the same sequence as or encoding the same polypeptide as a nematode MDH-like gene (other than the C. elegans MDH-like genes, MDH1 and MDH2).
Also featured are: 1) isolated nucleic acid molecules having a strand that hybridizes under low stringency conditions to a single stranded probe of the sequence of SEQ ID NO: 1 or 2 or their complements and, optionally, encodes a polypeptide of between 280 and 372 amino acids; 2) isolated nucleic acid molecules having a strand that hybridizes under high stringency conditions to a single stranded probe of the sequence of SEQ ID NO: 1 or 2 or their complements and, optionally, encodes a polypeptide of between 280 and 372 amino acids; 3) isolated nucleic acid fragments of MDH-like nucleic acid molecule, e.g., a fragment of SEQ ID NO:1 that is about 573, 575, 750, 1000, 1300, 1500, 1750, or more nucleotides in length or ranges between such lengths, or a fragment of SEQ ID NO:2 that is about 567, 575, 600, 750, 1000, 1300, 1500, 1750, or more nucleotides in length or ranges between such lengths; and 4) oligonucleotides that are complementary to an MDH-like nucleic acid molecule or an MDH-like nucleic acid complement, e.g., an oligonucleotide of about 10, 15, 18, 20, 22, 24, 28, 30, 35, 40, 50, 60, 70, 80, or more nucleotides in length. Exemplary oligonucleotides are oligonucleotides which anneal to a site located between a) nucleotides about 1 to 84, 61 to 84, 1081 to 1140, 1121 to 1200, 1081 to 1260 or 1201 to 1327 of SEQ ID NO:1; or b )nucleotides about 1 to 120,61 to 162, 1021 to 1120, 1081 to 1140, 1121 to 1200, 1081 to 1260, or 1081 to 2068 of SEQ ID NO:2. Nucleic acid fragments include the following non-limiting examples: fragments comprising the sequences of nucleotides about 1 to 660, 85 to 660, 660 to 1000, and 1001 to 1367 of SEQ ID NO:1 and 2. The isolated nucleic acid can further include a heterologous promoter operably linked to the MDH-like nucleic acid molecule.
In certain embodiments, the nucleic acid molecule encodes a polypeptide having a biological activity of a LMDH1 or MDH2 polypeptide, e.g., the ability to interconnect the substrates malate and oxaloacetate.
A molecule featured herein can be from a nematode of the class Araeolaimida, Ascaridida, Chromadorida, Desmodorida, Diplogasterida, Monhysterida, Mononchida, Oxyurida, Rhigonematida, Spirurida, Enoplia, Desmoscolecidae, or Tylenchida, Alternatively, the molecule can be from a species of the class Rhabditida, particularly a species other than C. elegans. 
In another aspect, the invention features a vector, e.g., a vector containing an aforementioned nucleic acid. The vector can further include one or more regulatory elements, e.g., a heterologous promoter. The regulatory elements can be operably linked to the MDH-like nucleic acid molecules in order to express an MDH-like nucleic acid molecule. In yet another aspect, the invention features a transgenic cell or transgenic organism having in its genome a transgene containing an aforementioned MDH-like nucleic acid molecule and a heterologous nucleic acid, e.g., a heterologous promoter.
In still another aspect, the invention features an antibody, e.g., an antibody, fragment, or derivative thereof that binds specifically to an aforementioned polypeptide. The specificity of the antibody can be such that it does not bind to a C. elegans MDH-like polypeptide. Such antibodies can be polyclonal or monoclonal antibodies. The antibodies can be modified, e.g., humanized, rearranged as a single-chain, or CDR-grafted. The antibodies may be directed against a fragment, a peptide, or a discontinuous epitope from an MDH-like polypeptide.
In another aspect, the invention features a method of screening for a compound that binds to a nematode MDH-like polypeptide, e.g., an aforementioned polypeptide. The method includes providing the nematode polypeptide; contacting the polypeptide with a test compound; and detecting binding of the test compound to the nematode polypeptide. In one embodiment, the method further includes contacting a plant or mammalian MDH-like polypeptide with the test compound; and detecting binding of the test compound to the plant or mammalian MDH-like polypeptide, e.g., a MDH-like polypeptide of tobacco, cotton, pepper, tomato, or human. A test compound that binds the nematode MDH-like polypeptide with at least 2-fold, 5-fold, 10-fold, 20-fold, 50-fold, or 100-fold tighter affinity relative to its affinity for the plant or mammalian MDH-like polypeptide can be identified. In another embodiment, the method further includes contacting nematode MDH-like polypeptide with the test compound and detecting an MDH-like activity, e.g., the ability to introconvert malate and oxaloacetate. A decrease in the level of MDH-like activity of the polypeptide relative to the level of MDH-like activity of the polypeptide in the absence of the test compound is an indication that the test compound is an inhibitor of the MDH-like activity. Such inhibitory compounds are potential selective agents for reducing the viability of a nematode expressing an MDH-like polypeptide., e.g., M. incognita. Preferably, the inhibitory compounds inhibit the MDH-like activity of both M. incognita MDH1 and MDH2.
Another featured method is a method of screening for a compound that alters an activity of an MDH-like polypeptide. The method includes providing the polypeptide; contacting a test compound to the polypeptide; and detecting an MDH-like activity, wherein a change in MDH-like activity relative to the MDH-like activity of the polypeptide in the absence of the test compound is an indication that the test compound alters the activity of the polypeptide. The method can further include contacting the test compound to a plant or mammalian MDH-like polypeptide; and measuring the MDH-like activity of the plant or mammalian MDH-like polypeptide. A test compound that alters the activity of the nematode MDH-like polypeptide at a given concentration and that does not substantially alter the activity of the plant or mammalian MDH-like polypeptide at the given concentration can be identified. An additional method includes screening for both binding to an MDH-like polypeptide and for alteration in activity of an MDH-like polypeptide.
Yet another featured method is a method of screening for a compound that alters the viability or fitness of a transgenic cell or organism. The transgenic cell or organism has a transgene that expresses an MDH-like polypeptide. The method includes contacting a test compound to the transgenic cell or organism; and detecting the viability or fitness of the transgenic cell or organism.
Also featured is a method of screening for a compound that alters the expression of a nematode nucleic acid encoding an MDH-like polypeptide, e.g., a nucleic acid encoding an M. incognita MDH-like polypeptide. The method includes contacting a cell, e.g., a nematode cell, with a test compound, and detecting expression of a nematode nucleic acid encoding an MDH-like polypeptide, e.g., by hybridization to a probe complementary to the nematode nucleic acid encoding an MDH-like polypeptide. Compounds identified by the method are also within the scope of the invention.
In yet another aspect, the invention features a method of treating a disorder caused by a nematode, e.g., M. incognita, in a subject, e.g., a host plant or host animal. The method includes administering to the subject an effective amount of an inhibitor of an MDH-like polypeptide activity or an inhibitor of expression of an MDH-like polypeptide. Non-limiting examples of such inhibitors include: an antisense nucleic acid (or PNA) to an MDH-like nucleic acid, an antibody to an MDH-like polypeptide, or a small molecule identified as an MDH-like polypeptide inhibitor by a method described herein.
A xe2x80x9cpurified polypeptidexe2x80x9d, as used herein, refers to a polypeptide that has been separated from other proteins, lipids, and nucleic acids with which it is naturally associated. The polypeptide can constitute at least 10, 20, 50 70, 80 or 95% by dry weight of the purified preparation.
An xe2x80x9cisolated nucleic acidxe2x80x9d is a nucleic acid, the structure of which is not identical to that of any naturally-occurring nucleic acid, or to that of any fragment of a naturally occurring genomic nucleic acid spanning more than three separate genes. The term therefore covers, for example: (a) a DNA which is part of a naturally occurring genomic DNA molecule but is not flanked by both of the nucleic acid sequences that flank that part of the molecule in the genome of the organism in which it naturally occurs; (b) a nucleic acid incorporated into a vector or into the genomic DNA of a prokaryote or eukaryote in a manner such that the resulting molecule is not identical to any naturally occurring vector or genomic DNA; (c) a separate molecule such as a cDNA, a genomic fragment, a fragment produced by polymerase chain reaction (PCR), or a restriction fragment; and (d) a recombinant nucleotide sequence that is part of a hybrid gene, i.e., a gene encoding a fusion protein. Specifically excluded from this definition are nucleic acids present in mixtures of different (i) DNA molecules, (ii) transfected cells, or (iii) cell clones: e.g., as these occur in a DNA library such as a cDNA or genomic DNA library. Isolated nucleic acid molecules according to the present invention further include molecules produced synthetically, as well as any nucleic acids that have been altered chemically and/or that have modified backbones.
Although the phrase xe2x80x9cnucleic acid moleculexe2x80x9d primarily refers to the physical nucleic acid molecule and the phrase xe2x80x9cnucleic acid sequencexe2x80x9d refers to the sequence of the nucleotides in the nucleic acid molecule, the two phrases can be used interchangeably.
The term xe2x80x9csubstantially purexe2x80x9d as used herein in reference to a given polypeptide means that the polypeptide is substantially free from other biological macromolecules. The substantially pure polypeptide is at least 75% (e.g., at least 80, 85, 95, or 99%) pure by dry weight. Purity can be measured by any appropriate standard method, for example, by column chromatography, polyacrylamide gel electrophoresis, or HPLC analysis.
The xe2x80x9cpercent identityxe2x80x9d of two amino acid sequences or of two nucleic acids is determined using the algorithm of Karlin and Altschul Proc. Natl. Acad. Sci. USA 87:2264-68, 1990, modified as in Karlin and Altschul Proc. Natl. Acad. Sci. USA 90:5873-77, 1993. Such an algorithm is incorporated into the BLASTN and BLASTX programs (version 2.0) of Altschul, et al. J. Mol. Biol. 215:403-10, 1990. BLAST nucleotide searches can be performed with the BLASTN program, score=100, wordlength=12 to obtain nucleotide sequences homologous to the nucleic acid molecules of the invention. BLAST protein searches can be performed with the BLASTX program, score=50, wordlength=3 to obtain amino acid sequences homologous to the protein molecules of the invention. Where gaps exist between two sequences, Gapped BLAST can be utilized as described in Altschul et al., Nucleic Acids Res. 25:3389-3402, 1997. When utilizing BLAST and Gapped BLAST programs, the default parameters of the respective programs (e.g., BLASTX and BLASTN) can be used. See http://www.ncbi.nlm.nih.gov.
As used herein, the term xe2x80x9ctransgenexe2x80x9d means a nucleic acid sequence (encoding, e.g., one or more subject polypeptides) which is partly or entirely heterologous, i.e., foreign, to the transgenic plant or cell into which it is introduced or is homologous to an endogenous gene of the transgenic plant or cell into which it is introduced, but which is designed to be inserted or is inserted into the plant""s genome in such a way as to alter the genome of the cell into which it is inserted (e.g., it is inserted at a location which differs from that of the natural gene or its insertion results in a knockout). A transgene can include one or more transcriptional regulatory sequences and any other nucleic acid, such as introns, that may be necessary for optimal expression of the selected nucleic acid, all operably linked to the selected nucleic acid, and may include an enhancer sequence.
As used herein, the term xe2x80x9ctransgenic cellxe2x80x9d refers to a cell containing a transgene.
As used herein, a xe2x80x9ctransgenic plantxe2x80x9d is any plant in which one or more, or all, of the cells of the plant includes a transgene. The transgene can be introduced into the cell, directly or indirectly by introduction into a precursor of the cell, by way of deliberate genetic manipulation, such as by T-DNA mediated transfer, electroporation, or protoplast transformation. The transgene may be integrated within a chromosome, or it may be extrachromosomally replicating DNA.
As used herein, the term xe2x80x9ctissue-specific promoterxe2x80x9d means a DNA sequence that serves as a promoter, i.e., regulates expression of a selected DNA sequence operably linked to the promoter, and which effects expression of the selected DNA sequence in specific cells of a tissue, such as a leaf, a root, or a stem.
As used herein, the terms xe2x80x9chybridizes under stringent conditionsxe2x80x9d and xe2x80x9chybridizes under high stringency conditionsxe2x80x9d refers to conditions for hybridization in 6xc3x97sodium chloride/sodium citrate (SSC) at about 45xe2x96xa1C., followed by two washes in 0.2xc3x97SSC, 0.1% SDS at 65xe2x96xa1C. As used herein, the term xe2x80x9chybridizes under low stringency conditionsxe2x80x9d refers to conditions for hybridization in 6xc3x97sodium chloride/sodium citrate (SSC) at about 45xe2x96xa1C, followed by two washes in 6xc3x97SSC buffer, 0. 1% (w/v) SDS at 2xe2x96xa1C.
A xe2x80x9cheterologous promoterxe2x80x9d, when operably linked to a nucleic acid sequence, refers to a promoter which is not naturally associated with the nucleic acid sequence.
As used herein, an agent with xe2x80x9canthelmintic activityxe2x80x9d is an agent which, when tested, has measurable nematode-killing activity or results in infertility or sterility in the nematodes such that inviable or no offspring result. In the assay, the agent is combined with nematodes, e.g., in a well of microtiter dish having agar media containing the agent. Staged adult nematodes are placed on the media The time of survival, viability of offspring, and/or the movement of the nematodes are measured. An agent with xe2x80x9canthelmintic activityxe2x80x9d reduces the survival time of adult nematodes relative to unexposed similarly-staged adults, e.g., by about 20%, 40%, 60%, 80%, or more. In the alternative, an agent with xe2x80x9canthelmintic activityxe2x80x9d may also cause the nematodes to cease replicating, regenerating, and/or producing viable progeny, e.g., by about 20%, 40%, 60%, 80%, or more.
As used herein, the term xe2x80x9cbindingxe2x80x9d refers to the ability of a first compound and a second compound that are not covalently attached to physically interact. The apparent dissociation constant for a binding event can be 1 mM or less, for example, 10 nM, 1 nM, 0.1 nM or less.
As used herein, the term xe2x80x9cbinds specificallyxe2x80x9d refers to the ability of an antibody to discriminate between a target ligand and a non-target ligand such that the antibody binds to the target ligand and not to the non-target ligand when simultaneously exposed to both the given ligand and non-target ligand, and when the target ligand and the non-target ligand are both present in a molar excess over the antibody.
A used herein, the term xe2x80x9caltering an activityxe2x80x9d refers to a change in level, either an increase or a decrease in the activity, particularly an MDH-like or MDH activity. The change can be detected in a qualitative or quantitative observation. If a quantitative observation is made, and if a comprehensive analysis is performed over a plurality of observations, one skilled in the art can apply routine statistical analysis to identify modulations where a level is changed and where the statistical parameter, the p value, is less than 0.05.
In part, the nematode MDH proteins and nucleic acids described herein are novel targets for anti-nematode vaccines, pesticides, and drugs. Inhibition of these molecules can provide means of inhibiting nematode metabolism and/or the nematode life-cycle.
All publications, patents, patent applications and other reference materials mentioned herein are incorporated by reference in their entirety.
The details of one or more embodiments of the invention are set forth in the accompanying drawings and the description below. Other features, objects, and advantages of the invention will be apparent from the description and drawings, and from the claims.